3D map of DNA reveals hidden loops that allow genes to work together

Every genome is a miracle of packaging. Somehow a human cell crams two meters of DNA into its tiny nucleus, and yet this tangled mess can carry out the complex task of building and maintaining our bodies. Now, the most detailed look yet at this genomic jumble reveals loops of DNA that bring distant parts of chromosomes together, allowing them to act in concert. The work could help researchers pin down the genetic causes of diseases and help clarify how the genome functions.

“It sheds a light in a dark room,” says Wouter de Laat, a molecular biologist at the Hubrecht Institutein Utrecht, the Netherlands. “It puts things into perspective.”

Genes and the rest of each chromosome's DNA are strung like beads on a necklace. To turn on—or off—a gene must connect up with the appropriate regulatory DNA that controls its activity, which can be quite far away on that necklace or even on another necklace. So for decades, molecular biologists have suspected that the way DNA folds up in the nucleus is key to making these connections at the right time and in the right place.

But only recently have they figured out the biochemical tricks needed to catch DNA in its folded state. Their first techniques enabled them to look at the position of a single piece of DNA, such as a gene.

In 2009, Erez Lieberman Aiden, a biologist now at Baylor College of Medicine (BCM) in Houston, Texas, and his colleagues came up with a method they called Hi-C to look at all the connections at once. They couldn't see much detail—only down to a million-base resolution, many times larger than the size of a gene—and simply discerned that the DNA segregated into two “compartments,” one with active DNA and one where the genes tended to be turned off. But researchers could use this technique only on DNA they had removed from the nucleus, which led to imprecise results.

Now, by figuring out how to do Hi-C on intact nuclei, BCM’s Suhas Rao and Miriam Huntley have drilled down deeper to get many more details. They can detect features as small as 1000 bases—smaller than a typical gene—and have come up with 3D DNA maps for eight lines of human cells, including cancer and basic tissues, and for one mouse cancer cell line. For one human lymphoid cancer cell line, for example, they detected 4.9 billion contacts between pairs of DNA pieces; for other cell types, the number of contacts ranged from 395 million to 1.1 billion. The more contacts between two particular pieces of DNA, the closer together those pieces are in 3D space.

Working with sophisticated computer programs, the researchers made these maps based on the contacts. They plotted how many times a pair of DNA pieces made contact and from those data determined where each piece of DNA was relative to all the rest of the DNA.

The genome is arranged into about 10,000 loops, Rao, Huntley, Aiden, and their colleagues report online today in Cell. A loop forms when two separated pieces of DNA come into close contact, with the loop being the DNA in between. In each cell type, different pieces of DNA come in contact, consequently changing the loops. These differences in structure may set up the different patterns of gene activity that define each cell type, Aiden explains. In the cells that come from female donors, the researchers also noticed gigantic loops in one of the X chromosomes—that loop likely silences that second X chromosome, as is necessary for the proper functioning of the still active X chromosome’s genes.

The group compared maps of the mouse and human cancer cells. The maps were very similar, with most of the same loops, indicating that the 3D arrangements that define a specific type of cell have not changed much during evolution, the researchers report.

“It opens up a new way of looking at biology,” says Vishy Iyer, a molecular biologist at the University of Texas, Austin. In a sense, these maps are the missing bridge between cellular views—made possible by looking through a microscope—and molecular views—made possible by sequencing—of the genome, Iyer says.

The Aiden lab has set up a website that works a little like Google Earth. Researchers can locate their favorite gene and drill down from compartment to loop to the DNA it touches.

“It’s a beautiful, endless resource to do many more analyses,” De Laat says. Countless studies of the genomes of people with conditions ranging from diabetes to schizophrenia have identified bits of the genome that increase the risk of getting those diseases. Often those sections are not parts of any gene but may help regulate a gene’s activity. Pinning down the regulated gene has been quite a challenge. Now, geneticists can check if the bits they identified are in contact with a potentially relevant gene. “It will greatly facilitate nailing down the genes that underlie diseases,” De Laat says.